Surfactant templating provides for the synthesis of ordered mesoporous silica and the opportunity to tailor the pore size, pore structure, particle morphology and surface functionality of the silica through the selection of synthesis conditions and surfactant template. This work extends the synthesis of nanostructured silica using fluorinated surfactant templates to the synthesis of organic/inorganic composites. The effect of fluorinated surfactant templates (C6F13C2H4NC5H5Cl, C8F17C2H4NC5H5Cl and C10F21C2H4NC5H5Cl), which have highly hydrophobic fluorocarbon tails, on functional group incorporation, accessibility, and silica textural properties is examined and compared to properties of hydrocarbon surfactant (C16H33N(CH3)3Br, CTAB) templated silica. Hydrocarbon (vinyl, n-decyl and 3-aminopropyl) and fluorocarbon (perfluoro-octyl, perfluorodecyl) functional group incorporation by direct synthesis is demonstrated, and its effects on silica properties are interpreted based on the aggregation behavior with the surfactant templates. Silica materials synthesized with CTAB possess greater pore order than materials synthesized with the fluorocarbon surfactants. The incorporation of the short vinyl chain substantially reduces silica pore size and pore order. However, pore order increases with functionalization for materials synthesized with the fluorinated surfactant having the longest hydrophobic chain. The incorporation of longer chain functional groups (n-decyl, perfluorodecyl, perfluoro-octyl) by direct synthesis results in hexagonal pore structured silica for combinations of hydrocarbon/fluorocarbon surfactant and functional groups. The long chain of these silica precursors, which can be incorporated in the surfactant micelle core, affect the pore size less than vinyl incorporation. Synthesis using the longer chain fluoro-surfactant (C8F17C2H4NC5H5Cl) template in ethanol/water solution results in highest incorporation of both n-decyl and the fluorocarbon functional groups, with a corresponding loss of material order in the fluorinated material. Matching the fluorocarbon surfactant (C6F13C2H4NC5H5Cl) to the perfluoro-octyl precursor did not show improved functional group incorporation. Higher incorporation of the perfluoro-octyl functional group was observed for all surfactant templates, but the perfluoro-decyl silica is a better adsorbent for the separation of hydrocarbon and fluorocarbon tagged anthraquinones. Incorporating a reactive hydrophilic functional group (3-aminopropyl) suggests further applications of the resulting nanoporous silica. Greater amine incorporation is achieved in the CTAB templated silica, which has hexagonal pore structure; the order and surface area decreases for the fluorinated surfactant templated material